Dataset Information

COVID-19 Surveillance in a Primary Care Sentinel Network: In-Pandemic Development of an Application Ontology.

ABSTRACT: BACKGROUND:Creating an ontology for COVID-19 surveillance should help ensure transparency and consistency. Ontologies formalize conceptualizations at either the domain or application level. Application ontologies cross domains and are specified through testable use cases. Our use case was an extension of the role of the Oxford Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) to monitor the current pandemic and become an in-pandemic research platform. OBJECTIVE:This study aimed to develop an application ontology for COVID-19 that can be deployed across the various use-case domains of the RCGP RSC research and surveillance activities. METHODS:We described our domain-specific use case. The actor was the RCGP RSC sentinel network, the system was the course of the COVID-19 pandemic, and the outcomes were the spread and effect of mitigation measures. We used our established 3-step method to develop the ontology, separating ontological concept development from code mapping and data extract validation. We developed a coding system-independent COVID-19 case identification algorithm. As there were no gold-standard pandemic surveillance ontologies, we conducted a rapid Delphi consensus exercise through the International Medical Informatics Association Primary Health Care Informatics working group and extended networks. RESULTS:Our use-case domains included primary care, public health, virology, clinical research, and clinical informatics. Our ontology supported (1) case identification, microbiological sampling, and health outcomes at an individual practice and at the national level; (2) feedback through a dashboard; (3) a national observatory; (4) regular updates for Public Health England; and (5) transformation of a sentinel network into a trial platform. We have identified a total of 19,115 people with a definite COVID-19 status, 5226 probable cases, and 74,293 people with possible COVID-19, within the RCGP RSC network (N=5,370,225). CONCLUSIONS:The underpinning structure of our ontological approach has coped with multiple clinical coding challenges. At a time when there is uncertainty about international comparisons, clarity about the basis on which case definitions and outcomes are made from routine data is essential.

SUBMITTER: de Lusignan S

PROVIDER: S-EPMC7674143 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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COVID-19 Surveillance in a Primary Care Sentinel Network: In-Pandemic Development of an Application Ontology.

de Lusignan Simon S Liyanage Harshana H McGagh Dylan D Jani Bhautesh Dinesh BD Bauwens Jorgen J Byford Rachel R Evans Dai D Fahey Tom T Greenhalgh Trisha T Jones Nicholas N Mair Frances S FS Okusi Cecilia C Parimalanathan Vaishnavi V Pell Jill P JP Sherlock Julian J Tamburis Oscar O Tripathy Manasa M Ferreira Filipa F Williams John J Hobbs F D Richard FDR

JMIR public health and surveillance 20201117 4

<h4>Background</h4>Creating an ontology for COVID-19 surveillance should help ensure transparency and consistency. Ontologies formalize conceptualizations at either the domain or application level. Application ontologies cross domains and are specified through testable use cases. Our use case was an extension of the role of the Oxford Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) to monitor the current pandemic and become an in-pandemic research platform.<h ...[more]

PMID: 33112762

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Project description:Colorectal cancer (CRC) is the third leading cause of cancer mortality in Switzerland, and kills 1600 people annually. Most deaths could be prevented by screening, but the 2012 Swiss national health survey found that only 40% of 50-75-year-olds had been tested within recommended intervals (26% with colonoscopy in the last 10 year, 7% with fecal occult blood test [FOBT] in the last 2 years, and 7% with both). If screening starts at age 50, in the average risk population absolute risk of dying from CRC at age 80 can be cut from 2% to 1%, reducing relative risk by 50%. Since 2013, Switzerland has reimbursed screening by colonoscopy every 10 years or FOBT every 2 years for adults 50-69 years old. Conforming to current recommendations, the Federal Office of Public Health (FOPH) officially recognizes both screening modalities. When patients are offered a choice of screening test (colonoscopy vs. FOBT), they are as likely to opt for one as the other. Patient preferences are unlikely to vary much between PCP practices, so distribution of colonoscopy and FOBT within each practice should also be roughly equal. Family physicians are recognized as the most trusted professional to discuss CRC screening in Switzerland. However, many primary care physicians (PCPs) prefer prescribing colonoscopy over FOBT, but physician preference for method seems to vary widely between regions. If physician preferences and local medical culture currently influence choice of method more strongly than patient preferences, encouraging PCPs to diagnose patient preferences for screening method may reduce the number of PCPs who prescribe only one method. An earlier study in Switzerland showed that training PCPs and giving them educational support and decision aids raised the number who intend to prescribe colonoscopy and FOBT in equal proportions. A randomized controlled trial in the US showed that when patients were offered both FOBT and colonoscopy rather than only colonoscopy alone, more patients were screened for CRC. Offering choice of method may thus increase overall screening rates. The Swiss Sentinel Surveillance Network (Sentinella) is a cooperative surveillance project including the Federal Office of Public Health (FOPH), PCPs representatives and the five Swiss institutes of family medicine. A sample of 150 to 250 general practitioners, internists and pediatricians in private practices from all regions of Switzerland report weekly morbidity data to the network using irreversibly anonymized patient data collected during consultations. In 2017, 91 out of 129 eligible PCPs of the Sentinella network participated in a cross-sectional data collection on CRC screening. The Sentinella network appears ideally suited to perform an intervention in order to modify screening practices and measure outcomes using the same collection form as in 2017. This study will test the benefits of a prepackaged training program in participatory medicine sent by post to PCPs in Switzerland. The package is designed to improve their diagnoses of patient preferences for screening and screening method (colonoscopy or FOBT). The study begins with the hypothesis that giving PCPs evidence summaries on CRC screening, decision aids for patients, and performance feedback on the 2017 data collection will increase the number of PCPs whose patients include at least one screened with FOBT, and who will prescribe at least one FOBT/FIT (Fecal Immunochemical Test) instead of prescribing only colonoscopy. This might reduce variation in care between PCP practices by increasing variation in methods of screening prescribed within each PCP practices. Analyses from the 2017 data collection suggest that fewer patients refused CRC testing in practices that offered both methods than in practices that offered only colonoscopy. This intervention might increase screening rates overall, while respecting patient’s autonomy to refuse the test and to be prescribed the test they prefer. The study will compare outcomes among PCPs allocated to the intervention group to those in the control group, and will be measured by collecting anonymous structured patient data on 40 consecutive patients by PCPs and questionnaires filled by PCPs. The study is designed to fit within the Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) framework for structuring data collection. RE-AIM ensures that a study’s outcomes for future implementation and dissemination works are collected. The RE-AIM criteria will be used to identify the translatability and public health impact of this intervention, and for making clear to future stakeholders the internal and external validity of study results.

Dataset Information

COVID-19 Surveillance in a Primary Care Sentinel Network: In-Pandemic Development of an Application Ontology.

Publications

COVID-19 Surveillance in a Primary Care Sentinel Network: In-Pandemic Development of an Application Ontology.

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